The TeraShake Computational Platform for Large-Scale Earthquake Simulations

Author(s):  
Yifeng Cui ◽  
Kim Olsen ◽  
Amit Chourasia ◽  
Reagan Moore ◽  
Philip Maechling ◽  
...  
2007 ◽  
Vol 5 (3) ◽  
pp. 295-302 ◽  
Author(s):  
Marcio Faerman ◽  
Reagan Moore ◽  
Yifeng Cui ◽  
Yuanfang Hu ◽  
Jing Zhu ◽  
...  

2018 ◽  
Author(s):  
Bohdan Khomtchouk ◽  
Kasra A Vand ◽  
William C Koehler ◽  
Diem-Trang Tran ◽  
Kai Middlebrook ◽  
...  

Cardiovascular disease (CVD) is the leading cause of death worldwide, causing over 17M deaths per year, which outpaces global cancer mortality rates. Despite these sobering statistics, the state-of-the-art in computational infrastructure to study datasets associated with CVD has lagged far behind public resources widely available in the oncology field, where improved data science and visualization methods have led to the development of large-scale cancer genomics resources like MSKCC's cBioPortal or NCI's Genomic Data Commons (GDC) Portal. Developing a similar user-friendly computational platform could significantly lower the barriers between complex CVD data and researchers who want rapid, intuitive, and high-quality visual access to molecular profiles and clinical attributes from existing CVD projects. Here we present HeartBioPortal: a publicly available web application that provides intuitive visualization, analysis, and downloads of large-scale CVD data currently focused on gene expression, genetic association, and ancestry information. By democratizing access to anonymized CVD data, HeartBioPortal's aim is to integrate relevant omics and clinical information across the biological dataverse to support CVD clinicians and researchers.


Author(s):  
Kwan-Liu Ma ◽  
Aleksander Stompel ◽  
Jacobo Bielak ◽  
Omar Ghattas ◽  
Eui Joong Kim

2010 ◽  
Vol 34-35 ◽  
pp. 1911-1915
Author(s):  
Jun Tang

Because the web is not only the platform for information exchange but also the computational platform based on JavaScript engine, every computer having installed modern browser on the Internet can easily access the web and execute some JavaScript programs. Under above conditions, we develop a lightweight distributed computing system based on the web and JavaScript technologies. Our system plays an intermediary role between the IT expert who has to solve large-scale computational problem and end users on the Internet. In the other words, people could easily cooperate with each other to finish complicated computational problem through the support of our system.


2019 ◽  
Author(s):  
Yang Pan ◽  
Alexander H. Lee ◽  
Harry T. Yang ◽  
Yuanyuan Wang ◽  
Yang Xu ◽  
...  

AbstractAberrant alternative splicing (AS) is widespread in cancer, leading to an extensive but largely unexploited repertoire of potential immunotherapy targets. Here we describe IRIS, a computational platform leveraging large-scale cancer and normal transcriptomics data to discover AS-derived tumor antigens for T-cell receptor (TCR) and chimeric antigen receptor T-cell (CAR-T) therapies. Applying IRIS to RNA-Seq data from 22 glioblastomas resected from patients, we identified candidate epitopes and validated their recognition by patient T cells, demonstrating IRIS’s utility for expanding targeted cancer immunotherapy.


2020 ◽  
Vol 50 (1) ◽  
pp. 155-176
Author(s):  
Andrea C. Riaño ◽  
Juan C. Reyes ◽  
Luis E. Yamín ◽  
Jacobo Bielak ◽  
Ricardo Taborda ◽  
...  

Author(s):  
Yifeng Cui ◽  
Reagan Moore ◽  
Kim Olsen ◽  
Amit Chourasia ◽  
Philip Maechling ◽  
...  

2018 ◽  
Author(s):  
Mariana Levi ◽  
Prasad Bandarkar ◽  
Huan Yang ◽  
Ailun Wang ◽  
Udayan Mohanty ◽  
...  

SummaryOver the last 20 years, the application of structure-based (Gō-like) models has ranged from protein folding with coarse-grained models to all-atom representations of large-scale molecular assemblies. While there are many variants that may be employed, the common feature of these models is that some (or all) of the stabilizing energetic interactions are defined based on knowledge of a particular experimentally-obtained conformation. With the generality of this approach, there was a need for a versatile computational platform for designing and implementing this class of models. To this end, the SMOG 2 software package provides an easy-to-use interface, where the user has full control of the model parameters. This software allows the user to edit XML-formatted files in order to provide definitions of new structure-based models. SMOG 2 reads these “template” files and maps the interactions onto specific structures, which are provided in PDB format. The force field files produced by SMOG 2 may then be used to perform simulations with a variety of popular molecular dynamics suites. In this chapter, we describe some of the key features of the SMOG 2 package, while providing examples and strategies for applying these techniques to complex (often large-scale) molecular assemblies, such as the ribosome.


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